This work investigates the influence of pulse modulation frequency ranging from 50 Hz–10 kHz on the helium RF atmospheric pressure plasma jet's fundamental characteristics. The impact of modulation frequency on plasma jet discharge behaviour, geometrical variation, reactive species emission, and plasma parameters (gas temperature Tg, electron excitation temperature Texc, and electron density (ne)) are studied using various diagnostics such as optical imaging, emission spectra, and thermal diagnostic. From the experiments, it is observed that operating the plasma jet at low pulse modulation frequencies (around 50 Hz) provides enhanced plasma dimensions, higher electron densities and greater optical emission from reactive species (viz., He I, O, OH, N2+, etc.) as compared to the higher modulation frequencies. Besides the low power consumption, three times less gas temperature of the modulated plasma jet than the continuous wave mode makes it more advantageous for the applications. Moreover, the influence of duty cycle (D) and applied RF power (P) on the plasma jet characteristics are also discussed. It is found that 10–40% duty cycle operation provides the most favourable attributes. More importantly, the concern of shorter plasma length in RF plasma jets is overcome by operating at 10–20% duty cycle with increased applied power. This work thoroughly characterizes helium atmospheric pressure RF plasma jet with a wide range of pulse mode operating parameters, which could help to select appropriate operating conditions for various industrial and biomedical applications.